If one small, properly located gated community does not violate rights of others, many small, properly located gated communities don't too.
But they do, in fact. This is where actually checking your theory with physical reality would help you a lot. Remember that requirement of yours, above, that closing one small road or excluding blacks from one small gas station did not violate their liberties? It was predicated on others being available. There are only so many roads, so many gas stations, so many motels, etc - as soon as enough white racist communities are on the landscape, blacks can no longer actually, physically, travel as whites can. The percentage is not nearly as high as you seem to imagine, either - many hospital emergency rooms can be significantly cut off if just a couple of intersections miles away are shut down, for example.
This happened, in the US. Allow yourself to acquire information, ok?
Your "sundown towns" are clearly not libertarian, but democratic. Some democratically elected city council or so decides this, and then the owners of gas stations, motels, restrooms are forced to reject black customers.
1) That's irrelevant to the point - the physical situation faced by black people is the same regardless.
2) That is not true, historically, in the US. The custom was usually by informal, unwritten, voluntary agreement among enough of the white racists to make it too expensive or dangerous to oppose, and communicated by informal social dealings. (Official, legally established "sundown towns" were found mostly toward the North, where enough white people on enough of the landscape were unfamiliar with that level of racism to make informal establishment uncertain for white people without a written law, signage, and so forth. In the South, no such clarifications and formalizations were necessary)
So you declare a whole group of people, united by their race and political ideas, to be unavoidably criminal,
Not unavoidably. Only if they commit the crime of depriving black people of civil liberties they enjoy themselves, say by establishing hundreds of town sized exclusion zones all over the landscape. The actions, not the ideas, are criminal.
Conceptually not that different from concentration camps for Jews.
If your conceptions fail to distinguish between the guards and the prisoners, fail to distinguish between the inside and the outside of the Camps, and so forth, you might be in that situation.
In some way one can see that the German bigots were imprisoning themselves as well as the Jews, much as the whites in the US were crippling their own lives as well as the lives of the blacks, much as the man who turns the key is locking himself out of the cell he is locking someone else in: but this kind of Zen insight is levels above the practical realities of town politics, motel management and the like.
antisemitism presents them as inherently bad and criminal, in particular that they would continue to rape German women or so, had they not been forbidden at gunpoint by the Nazi government. At least I do not see any important conceptual difference here (only a large one in degree). If you see one, explain.
The most significant differences are those of physical reality - for example, if the anti-Semites had been completely correct about "the Jews", not lying and slandering, some kind of imprisonment of Jews (or at least exclusion from the community) would have been justified.
The conceptual differences lie in how one's theory discovers and handles physical fact.
Liberals, more than most, emphasize attention to that, and more often place agreement with physical reality above agreement with theoretical prescription in their analysis of a situation. That's one of the virtues of liberalism, that libertarians (say) could benefit by recognizing.